AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene062200

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene062200.t1 MTR_1g077390 77.070 157 11 1 1 132 1 157 3.18e-81 236
MS.gene062200.t1 MTR_5g047580 58.974 156 39 1 1 131 1 156 1.13e-58 179
MS.gene062200.t1 MTR_1g077320 63.694 157 32 1 1 132 1 157 4.71e-58 177
MS.gene062200.t1 MTR_4g028720 61.783 157 35 1 1 132 1 157 2.21e-55 170
MS.gene062200.t1 MTR_7g011950 62.420 157 34 1 1 132 1 157 5.13e-55 169
MS.gene062200.t1 MTR_1g084950 59.615 156 38 1 1 131 1 156 1.71e-51 160
MS.gene062200.t1 MTR_1g077300 59.873 157 36 2 1 132 1 155 3.74e-49 154
MS.gene062200.t1 MTR_1g090697 49.032 155 54 1 1 130 1 155 5.40e-44 141
MS.gene062200.t1 MTR_1g090783 50.327 153 51 1 3 130 2 154 7.83e-44 141
MS.gene062200.t1 MTR_1g090710 48.718 156 54 2 1 130 1 156 9.20e-43 138
MS.gene062200.t1 MTR_5g047560 46.154 156 43 2 1 131 1 140 1.91e-37 124
MS.gene062200.t1 MTR_3g065100 42.675 157 64 1 1 131 1 157 5.08e-27 100
MS.gene062200.t1 MTR_5g075380 32.692 156 79 1 1 130 1 156 7.55e-27 98.2
MS.gene062200.t1 MTR_4g032620 33.117 154 76 2 1 127 1 154 2.56e-26 98.6
MS.gene062200.t1 MTR_3g466980 37.908 153 69 1 1 127 1 153 8.02e-26 97.1
MS.gene062200.t1 MTR_4g031910 39.103 156 68 2 1 129 1 156 3.48e-24 93.2
MS.gene062200.t1 MTR_3g466830 39.333 150 65 2 3 126 2 151 4.74e-24 90.9
MS.gene062200.t1 MTR_4g063790 33.333 159 79 2 1 132 1 159 5.07e-23 88.6
MS.gene062200.t1 MTR_8g036130 55.714 70 31 0 1 70 1 70 1.23e-22 89.4
MS.gene062200.t1 MTR_2g016210 36.424 151 69 3 1 124 1 151 2.18e-22 88.6
MS.gene062200.t1 MTR_3g031240 31.447 159 82 3 1 132 1 159 3.75e-22 86.7
MS.gene062200.t1 MTR_4g028800 57.143 63 25 1 1 63 1 61 5.34e-21 80.9
MS.gene062200.t1 MTR_4g032260 38.994 159 70 2 1 132 1 159 5.15e-19 78.2
MS.gene062200.t1 MTR_3g466890 36.424 151 70 2 3 127 2 152 5.44e-19 78.2
MS.gene062200.t1 MTR_3g031100 32.903 155 75 3 1 127 1 154 3.08e-18 77.8
MS.gene062200.t1 MTR_2g035610 50.000 86 41 1 1 84 1 86 7.02e-18 74.3
MS.gene062200.t1 MTR_4g032290 37.179 156 71 2 1 129 1 156 5.83e-17 74.3
MS.gene062200.t1 MTR_3g467080 29.560 159 85 2 1 132 1 159 6.26e-16 70.1
MS.gene062200.t1 MTR_4g019670 40.449 89 49 2 1 86 1 88 2.21e-13 65.9
MS.gene062200.t1 MTR_2g035580 35.366 82 53 0 1 82 1 82 4.56e-13 62.4
MS.gene062200.t1 MTR_7g106510 36.667 90 54 1 1 87 1 90 8.96e-13 64.3
MS.gene062200.t1 MTR_7g055800 33.654 104 45 2 1 93 1 91 1.90e-11 56.6
MS.gene062200.t1 MTR_3g465410 28.244 131 67 2 29 132 1 131 3.38e-11 57.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene062200.t1 AT3G05860 38.926 149 65 2 1 123 1 149 1.60e-25 96.3
MS.gene062200.t1 AT3G05860 51.852 81 38 1 1 81 1 80 3.67e-25 96.3
MS.gene062200.t1 AT3G05860 51.852 81 38 1 1 81 1 80 5.84e-25 95.9
MS.gene062200.t1 AT5G48670 42.208 154 61 3 1 127 1 153 4.60e-23 92.0
MS.gene062200.t1 AT5G26630 35.948 153 72 1 1 127 1 153 3.09e-21 85.1
MS.gene062200.t1 AT1G65330 52.113 71 34 0 3 73 2 72 7.40e-21 85.5
MS.gene062200.t1 AT1G65300 32.450 151 76 1 3 127 2 152 1.35e-20 84.7
MS.gene062200.t1 AT5G27960 40.187 107 38 1 4 84 2 108 4.24e-19 81.3
MS.gene062200.t1 AT5G26650 32.667 150 75 1 4 127 2 151 7.05e-19 81.3
MS.gene062200.t1 AT1G31630 29.677 155 82 3 3 131 2 155 1.06e-17 77.8
MS.gene062200.t1 AT1G22590 47.541 61 32 0 1 61 1 61 3.03e-17 73.6
MS.gene062200.t1 AT2G28700 37.113 97 56 2 1 93 1 96 1.75e-16 74.3
MS.gene062200.t1 AT1G31640 29.333 150 79 2 3 126 2 150 7.03e-15 70.1
MS.gene062200.t1 AT5G26580 39.583 96 46 1 1 84 1 96 3.75e-14 67.8
MS.gene062200.t1 AT2G40210 38.889 90 52 1 1 87 1 90 1.40e-12 63.5
MS.gene062200.t1 AT5G06500 45.312 64 35 0 1 64 1 64 4.84e-11 58.5

Find 25 sgRNAs with CRISPR-Local

Find 30 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGCCTTTCTTGCCGAATCAT+TGG 0.368149 1.1:+57920026 None:intergenic
TGTATGGCTCCCTCTAGATT+TGG 0.415378 1.1:+57919886 None:intergenic
CTCCAATGATTCGGCAAGAA+AGG 0.422860 1.1:-57920028 MS.gene062200:CDS
TCAAATCATCAGGCAACTCT+TGG 0.451496 1.1:+57919695 None:intergenic
AGAGAGCTCTCTATTCTTTG+TGG 0.458868 1.1:-57919964 MS.gene062200:CDS
AAATCTAGAGGGAGCCATAC+AGG 0.466931 1.1:-57919884 MS.gene062200:intron
TCTGTAACAGTCAAATCATC+AGG 0.472686 1.1:+57919685 None:intergenic
TTTCACCTTCTTCCTAGTCA+TGG 0.474514 1.1:+57920062 None:intergenic
AAAGAAGGGTATCATTAAGA+AGG 0.475254 1.1:-57919989 MS.gene062200:CDS
TGTTATAGAATCAAACGGAT+TGG 0.483520 1.1:+57919918 None:intergenic
ATACCTCTCAATCACCTGTA+TGG 0.492173 1.1:+57919870 None:intergenic
GCAGCAGATTACTAAAACCA+GGG 0.508508 1.1:-57919791 MS.gene062200:intron
GAATGAGCTGGACATTCATA+TGG 0.511354 1.1:-57919734 MS.gene062200:CDS
TGCAGCAGATTACTAAAACC+AGG 0.515480 1.1:-57919792 MS.gene062200:intron
TAGCTACAACAAGAGAAAGA+AGG 0.531524 1.1:-57920004 MS.gene062200:CDS
ACCTCTGTTATAGAATCAAA+CGG 0.538136 1.1:+57919913 None:intergenic
CGGATTGGAAATTATAGCAC+AGG 0.556765 1.1:+57919933 None:intergenic
AGCTACAACAAGAGAAAGAA+GGG 0.560386 1.1:-57920003 MS.gene062200:CDS
TCCGTTTGATTCTATAACAG+AGG 0.561391 1.1:-57919914 MS.gene062200:CDS
ACAGAATAATGAGAATGAGC+TGG 0.567812 1.1:-57919746 MS.gene062200:CDS
TTGGAAATTATAGCACAGGC+TGG 0.567823 1.1:+57919937 None:intergenic
AGAGGTGTGGCCAAATCTAG+AGG 0.598360 1.1:-57919896 MS.gene062200:CDS
AGCTGGACATTCATATGGTT+AGG 0.635359 1.1:-57919729 MS.gene062200:CDS
GAGGTGTGGCCAAATCTAGA+GGG 0.655326 1.1:-57919895 MS.gene062200:CDS
TTGATTCTATAACAGAGGTG+TGG 0.661112 1.1:-57919909 MS.gene062200:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
ACCTCTGTTATAGAATCAAA+CGG + chr1.1:57919759-57919778 None:intergenic 30.0%
GAAAAAGATGAAGGAAATTG+AGG - chr1.1:57920034-57920053 MS.gene062200:CDS 30.0%
GCTAATTGAGAAAAAGATGA+AGG - chr1.1:57920025-57920044 MS.gene062200:CDS 30.0%
TGTTATAGAATCAAACGGAT+TGG + chr1.1:57919754-57919773 None:intergenic 30.0%
! TGCTTTTATCTCCAATGATT+CGG - chr1.1:57919632-57919651 MS.gene062200:CDS 30.0%
!! AAAGAAGGGTATCATTAAGA+AGG - chr1.1:57919680-57919699 MS.gene062200:CDS 30.0%
ACAGAATAATGAGAATGAGC+TGG - chr1.1:57919923-57919942 MS.gene062200:CDS 35.0%
AGCTACAACAAGAGAAAGAA+GGG - chr1.1:57919666-57919685 MS.gene062200:CDS 35.0%
GCTGCAAAAGAAAACTTTCT+TGG + chr1.1:57919863-57919882 None:intergenic 35.0%
TAGCTACAACAAGAGAAAGA+AGG - chr1.1:57919665-57919684 MS.gene062200:CDS 35.0%
TCCGTTTGATTCTATAACAG+AGG - chr1.1:57919755-57919774 MS.gene062200:CDS 35.0%
TCTGTAACAGTCAAATCATC+AGG + chr1.1:57919987-57920006 None:intergenic 35.0%
TTGATTCTATAACAGAGGTG+TGG - chr1.1:57919760-57919779 MS.gene062200:CDS 35.0%
AGAGAGCTCTCTATTCTTTG+TGG - chr1.1:57919705-57919724 MS.gene062200:CDS 40.0%
AGCTGGACATTCATATGGTT+AGG - chr1.1:57919940-57919959 MS.gene062200:CDS 40.0%
ATACCTCTCAATCACCTGTA+TGG + chr1.1:57919802-57919821 None:intergenic 40.0%
GAATGAGCTGGACATTCATA+TGG - chr1.1:57919935-57919954 MS.gene062200:CDS 40.0%
GCAGCAGATTACTAAAACCA+GGG - chr1.1:57919878-57919897 MS.gene062200:intron 40.0%
TCAAATCATCAGGCAACTCT+TGG + chr1.1:57919977-57919996 None:intergenic 40.0%
TGCAGCAGATTACTAAAACC+AGG - chr1.1:57919877-57919896 MS.gene062200:intron 40.0%
TTGGAAATTATAGCACAGGC+TGG + chr1.1:57919735-57919754 None:intergenic 40.0%
! CGGATTGGAAATTATAGCAC+AGG + chr1.1:57919739-57919758 None:intergenic 40.0%
!!! TTGCTTTTCTAGTTGTTCCC+TGG + chr1.1:57919898-57919917 None:intergenic 40.0%
AAATCTAGAGGGAGCCATAC+AGG - chr1.1:57919785-57919804 MS.gene062200:CDS 45.0%
AGCCTTTCTTGCCGAATCAT+TGG + chr1.1:57919646-57919665 None:intergenic 45.0%
TGTATGGCTCCCTCTAGATT+TGG + chr1.1:57919786-57919805 None:intergenic 45.0%
! CTCCAATGATTCGGCAAGAA+AGG - chr1.1:57919641-57919660 MS.gene062200:CDS 45.0%
GAGCCATACAGGTGATTGAG+AGG - chr1.1:57919796-57919815 MS.gene062200:intron 50.0%
GAGGTGTGGCCAAATCTAGA+GGG - chr1.1:57919774-57919793 MS.gene062200:CDS 50.0%
! AGAGGTGTGGCCAAATCTAG+AGG - chr1.1:57919773-57919792 MS.gene062200:CDS 50.0%


Chromosome Type Strat End Strand Name
chr1.1 gene 57919609 57920082 57919609 ID=MS.gene062200
chr1.1 mRNA 57919609 57920082 57919609 ID=MS.gene062200.t1;Parent=MS.gene062200
chr1.1 exon 57919885 57920082 57919885 ID=MS.gene062200.t1.exon1;Parent=MS.gene062200.t1
chr1.1 CDS 57919885 57920082 57919885 ID=cds.MS.gene062200.t1;Parent=MS.gene062200.t1
chr1.1 exon 57919609 57919809 57919609 ID=MS.gene062200.t1.exon2;Parent=MS.gene062200.t1
chr1.1 CDS 57919609 57919809 57919609 ID=cds.MS.gene062200.t1;Parent=MS.gene062200.t1
Gene Sequence

>MS.gene062200

ATGACTAGGAAGAAGGTGAAACTTGCTTTTATCTCCAATGATTCGGCAAGAAAGGCTAGCTACAACAAGAGAAAGAAGGGTATCATTAAGAAGGTGAGAGAGCTCTCTATTCTTTGTGGTATTCCAGCCTGTGCTATAATTTCCAATCCGTTTGATTCTATAACAGAGGTGTGGCCAAATCTAGAGGGAGCCATACAGGTGATTGAGAGGTATCAAAATGCATATATCAAACACAAGAAAAATAATGTGAACCAAGAAAGTTTTCTTTTGCAGCAGATTACTAAAACCAGGGAACAACTAGAAAAGCAAAGACAACAGAATAATGAGAATGAGCTGGACATTCATATGGTTAGGCACTTGCAAAACCAAGAGTTGCCTGATGATTTGACTGTTACAGATTTAAGAGATTATGATAAGCTAATTGAGAAAAAGATGAAGGAAATTGAGGACAAGATTGTTGCACTCAGTTTATGA
Protein sequence

>MS.gene062200.t1

MTRKKVKLAFISNDSARKASYNKRKKGIIKKVRELSILCGIPACAIISNPFDSITEVWPNLEGAIQQITKTREQLEKQRQQNNENELDIHMVRHLQNQELPDDLTVTDLRDYDKLIEKKMKEIEDKIVALSL